POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2VJZ
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.5
    Details pH 7.5
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 79.82 α = 90
    b = 79.82 β = 90
    c = 36.71 γ = 120
     
    Space Group
    Space Group Name:    H 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Details MICRO FOCUS
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength 0.9183
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.8
    Resolution(Low) 32.4
    Number Reflections(Observed) 33133
    Percent Possible(Observed) 96.8
    R Merge I(Observed) 0.11
    Redundancy 4.5
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.9
    Percent Possible(All) 84.4
    R Merge I(Observed) 0.54
    Mean I Over Sigma(Observed) 1.8
    Redundancy 2.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 32.43
    Number of Reflections(Observed) 7433
    Number of Reflections(R-Free) 391
    Percent Reflections(Observed) 96.8
    R-Factor(Observed) 0.175
    R-Work 0.172
    R-Free 0.239
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.64
    Anisotropic B[1][1] -0.28
    Anisotropic B[1][2] -0.14
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.28
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.43
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.85
    Number of Reflections(R-Free) 22
    Number of Reflections(R-Work) 419
    R-Factor(R-Work) 0.335
    R-Factor(R-Free) 0.329
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.545
    r_scbond_it 2.061
    r_mcangle_it 1.085
    r_mcbond_it 0.936
    r_nbd_refined 0.205
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.007
    r_chiral_restr 0.089
    r_dihedral_angle_4_deg 9.904
    r_dihedral_angle_3_deg 11.807
    r_dihedral_angle_2_deg 35.635
    r_dihedral_angle_1_deg 6.342
    r_angle_other_deg 0.959
    r_angle_refined_deg 1.425
    r_bond_other_d 0.001
    r_bond_refined_d 0.015
    r_nbd_other 0.181
    r_nbtor_refined 0.189
    r_nbtor_other 0.09
    r_xyhbond_nbd_refined 0.276
    r_symmetry_vdw_refined 0.227
    r_symmetry_vdw_other 0.171
    r_symmetry_hbond_refined 0.414
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 785
    Nucleic Acid Atoms 0
    Heterogen Atoms 6
    Solvent Atoms 97
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution AMORE
    Structure Refinement REFMAC 5.3.0040
     
    Software
    refinement REFMAC version: 5.3.0040
    model building AMORE